Antimicrobial resistance profile and multidrug resistance patterns of Streptococcus pneumoniae isolates from patients suspected of pneumococcal infections in Ethiopia.

BACKGROUND: Antimicrobial-resistant strains of Streptococcus pneumoniae have become one of the greatest challenges to global public health today and inappropriate use of antibiotics and high level of antibiotic use is probably the main factor driving the emergence of resistance worldwide. The aim of this study is, therefore, to assess the antimicrobial resistance profiles and multidrug resistance patterns of S. pneumoniae isolates from patients suspected of pneumococcal infections in Ethiopia. METHODS: A hospital-based prospective study was conducted from January 2018 to December 2019 at Addis Ababa city and Amhara National Region State Referral Hospitals. Antimicrobial resistance tests were performed from isolates of S. pneumoniae that were collected from pediatric and adult patients. Samples (cerebrospinal fluid, blood, sputum, eye discharge, ear discharge, and pleural and peritoneal fluids) from all collection sites were initially cultured on 5% sheep blood agar plates and incubated overnight at 37 °C in a 5% CO2 atmosphere. Streptococcus pneumoniae was identified and confirmed by typical colony morphology, alpha-hemolysis, Gram staining, optochin susceptibility, and bile solubility test. Drug resistance testing was performed using the E-test method according to recommendations of the Clinical and Laboratory Standards Institute. RESULTS: Of the 57 isolates, 17.5% were fully resistant to penicillin. The corresponding value for both cefotaxime and ceftriaxone was 1.8%. Resistance rates to erythromycin, clindamycin, tetracycline, chloramphenicol and trimethoprim-sulfamethoxazole were 59.6%, 17.5%, 38.6%, 17.5 and 24.6%, respectively. Multidrug resistance (MDR) was seen in 33.3% isolates. The most common pattern was co-resistance to penicillin, erythromycin, clindamycin, and tetracycline. CONCLUSIONS: Most S. pneumoniae isolates were susceptible to ceftriaxone and cefotaxime. Penicillin has been used as a drug of choice for treating S. pneumoniae infection. However, antimicrobial resistance including multidrug resistance was observed to several commonly used antibiotics including penicillin. Hence, it is important to periodically monitor the antimicrobial resistance patterns to select empirical treatments for better management of pneumococcal infection.

Serotype Distribution of Streptococcus pneumoniae Isolates Causing Invasive and Non-Invasive Infections Using Whole-Genome Sequencing in Ethiopia.

BACKGROUND: In Ethiopia, pneumococcal conjugate vaccine 10 (PCV10) was introduced in 2011 in the national vaccination program. This study was aimed to assess serotype distribution of invasive and non-invasive Streptococcus pneumoniae isolates using whole-genome sequencing. METHODS: A hospital-based prospective study was conducted from 2018 to 2019 at Addis Ababa and Amhara region referral hospitals, from all patients. Clinical Samples were collected and initially cultured onto 5% sheep blood agar at 37°C in a 5% CO2 atmosphere. Sequencing was done using the Illumina NextSeq 500 and SeroBA was used to predict serotypes from whole-genome sequencing raw data. RESULTS: Of the 57 S. pneumoniae isolates, there were 32 circulating serotypes. The most common serotypes were 15A/B/C (n=5, 8.8%), 6A (n=4, 7.0%), 10A/F (n=4, 7.0%), 23A (n=4, 7.0%) and 7C (n=3, 5.3%). The serotype coverage of PCV10 and PCV13 were 12.3% and 26.3% respectively. The most common invasive serotypes were 15A/B/C (n=5, 8.8%) and 6A (n=4, 7.0%), and non-invasive serotypes were 23A (n=4, 7.0%) and 10A/F (n=3, 5.3%). The most prevalent serotype obtained from PCV10 eligible children was 3 (n=2, 3.5%). The prevalent serotype obtained from PCV10 non-eligible patients were type 23A (n=4, 7%) and type 6A (n=3, 5.2%). The most common serotypes among children ≤18 years old were 10A/F, 7C, 35A/B, 16F, 19A, 3 and 38. However, the proportions of some non-vaccine serotypes (11A/B and 15A/B/C) were higher in adult patients. CONCLUSION: In this study a shift in the distribution of non-vaccinated S. pneumoniae serotypes increases in the population, and PCV10 serotype coverage was reduced as compared to PCV13. Therefore, it is important to continue monitoring serotype changes among all patients in addition to assessing the impact and effectiveness brought by vaccines and provides a foundation for prevention strategies and vaccine policies.